Contacts of the helix formed by residues 21 - 25 (chain D) in PDB entry 3NBN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D LEU* 3.9 9.0 - - + -
18D THR* 3.1 18.1 + - - +
20D GLU* 1.3 77.3 - - - +
22D MET* 1.3 63.9 + - - +
24D ASN* 3.3 22.5 - - - +
25D TYR* 3.6 4.7 + - - +
327D TYR* 5.6 0.7 - - - -
329D GLY* 3.2 31.5 - - - +
330D MET* 3.6 11.7 - - + -
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Residues in contact with MET 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 3.6 29.1 - - + +
18D THR 3.2 7.2 + - - +
19D ARG 4.1 2.9 - - - +
20D GLU 2.7 4.0 + - - -
21D ALA* 1.3 71.7 - - - +
23D ARG* 1.3 53.7 + - - +
24D ASN 2.7 4.3 + - - -
25D TYR* 2.5 36.9 + - - +
26D LEU* 3.2 35.2 + - + -
371D TRP* 3.9 15.3 - - + -
373D GLY 3.8 17.3 - - - +
374D ASP* 3.9 11.2 - - - -
413D THR* 4.5 11.7 - - + -
415D VAL* 3.7 24.5 - - + -
421D ILE* 3.9 22.9 - - + -
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ARG* 2.7 56.4 + - - +
20D GLU* 2.9 47.2 + - - +
22D MET* 1.3 74.8 - - - +
24D ASN* 1.3 64.3 + - - +
25D TYR 3.3 2.5 + - - -
26D LEU* 3.7 11.6 + - - +
27D LYS* 3.2 42.3 + - - +
374D ASP* 3.3 25.4 + - + -
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Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU* 3.3 28.0 + - - +
21D ALA* 3.3 15.1 - - - +
22D MET 2.7 4.5 + - - -
23D ARG* 1.3 83.3 + - - +
25D TYR* 1.3 54.4 + - - +
27D LYS* 4.5 12.6 - - - +
28D GLU* 3.3 29.1 + - - +
327D TYR* 4.1 6.8 + - - -
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Residues in contact with TYR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 6.5 0.2 - - + -
21D ALA 3.9 5.4 - - - +
22D MET* 2.5 20.5 + - - +
24D ASN* 1.3 73.7 - - - +
26D LEU* 1.3 72.9 + - + +
27D LYS 3.0 4.0 - - - -
28D GLU* 4.1 4.9 - - - +
29D ARG* 2.7 68.8 + - - +
31D ASP* 3.1 23.9 + - - -
327D TYR* 3.3 58.6 - + + -
329D GLY* 6.2 0.4 - - - -
413D THR* 5.6 5.2 - - + -
421D ILE* 3.5 28.0 - - + +
423D SER* 3.3 20.6 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il